Genome Databases

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Genome Databases
Genomics, Bioinformatics Medicine http//biochem
158.stanford.edu/
Doug Brutlag Professor Emeritus of Biochemistry
Medicine Stanford University School of Medicine
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Components of a Typical Human Gene
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Active Genes are Transcribed into RNA
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Splicing Transcript Yields Mature mRNA
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Mature mRNA contains Coding Region and 5 and 3
Untranslated Regions
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Mature mRNA contains7-Methyl-Guanosine 5 Cap
and 3 Poly A Tail
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ESTs, Full Length cDNAUniGene RefSeq Databases
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ESTs, Full Length cDNAUniGene RefSeq Databases
5 UTR
3 UTR
5 UTR
3 UTR
Protein
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GENSCAN Gene Modelhttp//genes.mit.edu/GENSCAN.ht
ml
Hidden Markov models of gene structure
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Genome Databases
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Entrez Gene Loci http//www.ncbi.nlm.nih.gov/entre
z/query.fcgi?dbgene
Entrez Gene
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Alternative Splicing GeneratesDistinct Proteins
in Different Tissues
Intron
Intron
Exon
Exon
Exon
Promoter
Terminator
Gene
Transcript
Splicing
mRNA-1
3
5
Alternate Splicing
Transcript
mRNA-2
5
3
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Alternative SplicingDetected in EST Libraries
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NCBI Genomeshttp//www.ncbi.nlm.nih.gov/sites/ent
rez?dbgenome
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Eukaryote Genome Projectshttp//www.ncbi.nlm.nih.
gov/genomes/leuks.cgi
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Canis lupus familiaris Genomehttp//www.ncbi.nlm.
nih.gov/sites/entrez?dbbioprojectcmdRetrievedo
ptOverviewlist_uids10726
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NCBI Entrez Genehttp//www.ncbi.nlm.nih.gov/sites
/entrez?dbgene
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NCBI Entrez Gene Human Opsinhttp//www.ncbi.nlm.
nih.gov/gene?termhuman20opsin
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Entrez Gene Human Opsin OPN1MWhttp//www.ncbi.nl
m.nih.gov/gene/2652
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Entrez Gene Human Opsin OPN1MWhttp//www.ncbi.nl
m.nih.gov/gene/2652
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MapViewer Human Opsin OPN1MWhttp//www.ncbi.nlm.
nih.gov/gene/2652
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Evidence Viewer for OPN1MWhttp//www.ncbi.nlm.nih
.gov/sutils/evv.cgi?taxid9606contigNT_167198.1
geneOPN1MWlid2652from4366022to4380289
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OMIM Home Pagehttp//www.ncbi.nlm.nih.gov/entrez/
query.fcgi?dbOMIM
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Colorblindness in OMIM
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Colorblindness in OMIMhttp//omim.org/entry/30380
0
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Colorblindness in OMIMhttp//omim.org/entry/30380
0
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Human Genome Resourceshttp//www.ncbi.nlm.nih.gov
/genome/guide/human/
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RefSeqhttp//www.ncbi.nlm.nih.gov/RefSeq/
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RefSeq Genehttp//www.ncbi.nlm.nih.gov/refseq/rsg
/
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NCBI UniGenehttp//www.ncbi.nlm.nih.gov/sites/ent
rez?dbunigene
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NCBI Homologene Databasehttp//www.ncbi.nlm.nih.g
ov/homologene
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Comparative Genomics
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Ensembl Home Pagehttp//www.ensembl.org/
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EBI Genomes Home Pagehttp//www.ensembl.org/
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Ensembl Human Genomehttp//www.ensembl.org/Homo_s
apiens/
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Ensembl Human Opsin Searchhttp//uswest.ensembl.o
rg/Homo_sapiens/Search/Results?speciesHomo_sapien
sidxqopsin
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Ensembl Human Opsin Geneshttp//uswest.ensembl.or
g/Homo_sapiens/Search/Results?speciesHomo_sapiens
idxqopsin
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Ensembl Human OPN1MW Genehttp//uswest.ensembl.or
g/Homo_sapiens/Gene/Summary?gENSG00000147380rX
153448107-153461633
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Ensembl Opsin OPN1MW Gene Locationhttp//uswest.e
nsembl.org/Homo_sapiens/Location/View?hHavana20g
enerX153448107-153461633rX153448109-15346163
2
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Ensembl OPN1MW Transcriptshttp//uswest.ensembl.o
rg/Homo_sapiens/Location/View?hHavana20generX
153448107-153461633rX153448109-153461632
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Ensembl OPN1MW Opsin Proteinhttp//uswest.ensembl
.org/Homo_sapiens/Transcript/ProteinSummary?dbcor
egENSG00000147380rX153448107-153461633tENST
00000369935
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Ensembl Tutorialshttp//uswest.ensembl.org/info/w
ebsite/tutorials/index.html
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UCSC Genome Home Pagehttp//genome.ucsc.edu/
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UCSC Genome Browserhttp//genome.ucsc.edu/cgi-bin
/hgGateway
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UCSC Genome Browserhttp//genome.ucsc.edu/cgi-bin
/hgGateway
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UCSC Genome Browserhttp//genome.ucsc.edu/cgi-bin
/hgTracks?positionchrX153485203-153499469hgsid
216983641knownGenepackhgFind.matchesuc004fkd.2
,
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UCSC Genome Browserhttp//genome.ucsc.edu/cgi-bin
/hgTracks?positionchrX153485203-153499469hgsid
216983641knownGenepackhgFind.matchesuc004fkd.2
,
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UCSC Proteome Browserhttp//genome.ucsc.edu/cgi-b
in/pbGateway
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UCSC Proteome Browserhttp//genome.ucsc.edu/cgi-b
in/pbGateway
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UCSC Help Filehttp//genome.ucsc.edu/goldenPath/h
elp/hgTracksHelp.html